Wikipedia:USEP/Courses/JHU MolBio Ogg FA13/Group 84E

Group 84E
This is a group page for the 410.602 Johns Hopkins Molecular Biology, section 84 course. This group will be working on the article TBD.

Use the talk page here to collaborate as a group, when learning to use and navigate Wikipedia, assessing articles, or for any other topic.

Use this page (not the talk page) for article assessments; rationale for selecting an article; etc (as specified in the milestone summary chart.

Please create a new section here for each of those assignments.

Article 1: Leucine Zipper
This article is listed as a "stub" article on the quality scale. It has basic information, listing only an introduction, a brief description of the leucine zipper's structure, and some general examples of leucine zippers and their role as regulatory proteins. The article does include a nice picture of a leucine zipper interacting with DNA. However, it needs improvements in order to achieve "Good Article" quality. While the article seems to be well written, neutral, and stable, it needs more references. Right now, it has two references and only has two inline citations.

Furthermore, the talk page has not been modified since 2008, and the discussion listed is very limited. There was a brief conversation regarding whether leucine zippers were DNA binding domains, but the situation was resolved within a day. Possible additional sources for this article include:

1) Weaver, Robert (2005). Molecular biology. New York: McGraw-Hill. ISBN 0-07-284611-9.

2) Lodish, Harvey et al. (2004). Molecular Cell Biology. New York: W.H. Freeman and Company. ISBN 0-7167-4366-3

3) Fordyce, PM et al. (2012). "Basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses." Proc Natl Acad Sci USA 109(45):E3084-93. . Link: http://www.ncbi.nlm.nih.gov/pubmed/?term=23054834

The first two references listed would provide further basic information regarding leucine zippers. The third reference would provide a specific example of a leucine zipper as a transcription factor.

Article 2: Biosynthesis
This article is listed as a "stub" article. It has a promising start, but it's very short, consisting of a single section. Despite its brevity, I found that there are some shortcomings. For example, some of the sentences are awkwardly stated and need to be rearranged. However, this may be rectified by restructuring the article and adding more sections. To elevate this article to "Good Article" status, additional references are also necessary. Currently, there are only three references, each used as an inline citation once. Illustrations or diagrams would enhance the article, making the material easier to understand.

In terms of the talk page, it's very stable, and it has not been updated since 2007. Nevertheless, the discussion within the talk page does not specifically address points to improve the article; it mostly discusses whether to merge the article with a different topic.

Possible additional sources to expand this article include:

1) Mann, John (1995). Chemical Aspects of Biosynthesis. New York: Oxford University Press. ISBN 978-0198556763

2) Nelson, David L et al (2012). Lehninger Principles of Biochemistry. New York: W.H. Freeman. ISBN 978-1429234146

3) Jones, PJ. (1997). "Regulation of cholesterol biosynthesis by diet in humans." Am J Clin Nutr 66(2):438-446. Link: http://ajcn.nutrition.org/content/66/2/438.abstract

The first two references would provide more information for the introduction of the article. Additionally because the first reference is a book that focuses on biosynthesis, it could prove to be an invaluable source in terms of providing generalizations and examples. Lastly, the third source could provide a more specific example regarding the biosynthesis of cholesterol.

Article 1: Ubiquitin-Conjugating Enzyme
At first glance the lead section of "Ubiquitin-conjugating enzyme" article is clearly in need of inline citation. Furthermore, I only see two references in the reference section. The limited references and the lack of inline citation may lead to statement in article being challenged. The article is clearly not an original research. The article has limited scope of coverage. I would have liked if the article defined the enzyme within the context of cellular function. In addition, the article does not present any protein structure for the protein form the Protein Data Bank. Furthermore, there is no ongoing discussions by editors on the talk page of the article. It needs more images and proper citation for the presented image. If the article made the above improvements and the recommended section guideline for molecular biology, it could achieve an improved article quality grading.

I believe the following review articles would be a good place to start to improve this article. The article “Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b, wild-type” Pdb ID: 2ESK, show the wild type X-ray diffraction structure of human Ubiquitin conjugating enzyme at 1.36A resolution.

I also found the review article “Effete, an E2 ubiquitin-conjugating enzyme with multiple roles in Drosophila development and chromatin organization”, which revises the function of E2 within cellular context. PMID: 24088712

Furthermore, the review article “Enzymes of ubiquitination and deubiquitination” also has more information about Ubiquition conjugating enzyme. PMID: 22708562

Article 2: Exoenzyme
The "Exoenzyme" article only has a lead section, and does not include the recommended sections of molecular and cellular biology style guide. it does not have any references. Furthermore, it does not have the necessary inline citations, which could lead to the statements of the article being challenged. However, the article presents a notable topic for discussion, and is not an original research. The article contains only a definition of the title, and does not have any of the necessary explanation for an online encyclopedia. It needs more details. The article does not include any images, such as protein structure or images to show molecular mechanism. Furthermore, there is no ongoing discussions by editors on the talk page of the article.

I was able to find an article that discusses the extra cellular enzymes that are present in soil, which are produced by the abundant number of microorganisms within the soil.

1. Skuji&ncedil; š, J., and R. G. Burns. "Extracellular enzymes in soil." Critical Reviews in Microbiology 4.4 (1976): 383-421.

I also found another article that talks about bacteria producing hydrolytic extracellular enzymes.

2. Sánchez-Porro, C., Martín, S., Mellado, E. and Ventosa, A. (2003), Diversity of moderately halophilic bacteria producing extracellular hydrolytic enzymes. Journal of Applied Microbiology, 94: 295–300. doi: 10.1046/j.1365-2672.2003.01834.x

Article Selection Rationale
We ultimately chose “Biosynthesis” as our article because our group liked the broadness that the topic provides. While the article needs a lot of work in terms of content, material and restructuring, we feel that this topic is very relevant to our Molecular Biology course. Furthermore, the scope of the topic is general enough such that our group can potentially find a wealth of information from numerous sources. This will allow us to gather enough material for different sections of the article. Not to mention, the stub already contains some promising information that can potentially be developed into its own sections. For example, the article mentions the organelles that are involved in biosynthesis, but it does not expand on their specific roles; this can potentially be converted into one of the sections for our article.

We believe that the article is noteworthy enough and deserves to be included as a Wikipedia article. Therefore, our task for this article is to write the article in such a way that it discusses the topic fully and in a well referenced manner. We will defining the article structure, including appropriate supporting images and diagrams, and presenting the material content appropriately, so that a general audience can understand the material.

Additionally, our group believes that the biosynthesis article is interesting and general enough to explore different facets of biosynthesis. We’ll have the opportunity to explore multiple varied examples that follow the anabolism of monomers to macromolecules, illustrate and learn about the pathways that lead to these polymers, and link key words in our article to other entries within Wikipedia. For these reasons, “Biosynthesis” seemed like an ideal choice for us.

Unit 8 Progress Report

 * Added prose contribution: modified and added to introduction, added a lipid and nucleotide sections
 * Incorporated images from Wikimedia Commons in lipid and nucleotide sections

Unit 10 Progress Report

 * Added prose contribution: finished lipid and nucleotide section, added DNA section, and made suggested changes recommended by reviewers
 * Incorporated an images from Wikimedia Commons for the lipid, nucleotide and DNA section
 * Used 4 additional references

Unit 12 Progress Report

 * Added prose contribution: Added a amino acids section, protein synthesis section, chemical properties section, and see also section; incorporated reviewers' suggestions.
 * Incorporated images from Wikimedia Commons for the amino acids and protein synthesis sections
 * Made equations for the chemical properties section and tRNA charging
 * Added a "multiple images" box for the nucleotides section
 * Created a "key players" table for translation section
 * Incorporated 21 new sources

Final Progress Report

 * Rewrote and expanded the original lead section
 * Kept one original source and added 62 sources
 * Added, formatted, and resized all of the images in the article
 * Made the equations in the “Properties of chemical reactions” and "Proteins" sections
 * Made the table found in the “Translation in steps” section
 * Added a total of 8 headings (and multiple subheadings)
 * Frequently interacted with the OA and other peer reviewers; responded to all comments and incorporated many of the reviewer’s suggestions to improve the article (Note: the OA was particularly helpful in relaying the formatting nuances that are required of Wikipedia articles.)